hpcflow.sdk.persistence.json.JSONPersistentStore

class hpcflow.sdk.persistence.json.JSONPersistentStore(app, workflow, path, fs)

Bases: PersistentStore[JsonStoreTask, JsonStoreElement, JsonStoreElementIter, JsonStoreEAR, StoreParameter]

A store that writes JSON files for all its state serialization.

Methods

add_EAR	Add a new EAR to an element iteration.
add_element	Add a new element to a task.
add_element_iteration	Add a new iteration to an element.
add_element_set	Add an element set to a task.
add_file	Add a file that will be associated with a parameter.
add_loop	Add a new loop to the workflow.
add_set_parameter	Add a parameter that is set to a value.
add_submission	Add a new submission.
add_submission_part	Add a submission part.
add_task	Add a new task to the workflow.
add_template_components	Add template components to the workflow.
add_unset_parameter	Add a parameter that is not set to any value.
cache_ctx	Context manager for using the persistent element/iteration/run cache.
cached_load	Context manager to cache the metadata.
check_parameters_exist	For each parameter ID, return True if it exists, else False.
copy	Copy the workflow store.
delete	Delete the persistent workflow.
delete_no_confirm	Permanently delete the workflow data with no confirmation.
get_EAR_skipped	Whether the element action run with the given ID was skipped.
get_EARs	Get element action runs with the given IDs.
get_creation_info	Get information about the creation of the workflow.
get_element_iterations	Get element iterations with the given IDs.
get_elements	Get elements with the given IDs.
get_loops	Retrieve all loops, including pending.
get_loops_by_IDs	Retrieve loops by index (ID), including pending.
get_name	Get the name of the workflow.
get_parameter_set_statuses	Get whether the parameters with the given IDs are set.
get_parameter_sources	Get the sources of the parameters with the given IDs.
get_parameters	Get parameters with the given IDs.
get_submissions	Retrieve all submissions, including pending.
get_submissions_by_ID	Get submissions with the given IDs.
get_task	Get a task.
get_task_elements	Get element data by an indices within a given task.
get_tasks	Retrieve all tasks, including pending.
get_tasks_by_IDs	Get tasks with the given IDs.
get_template	Get the workflow template.
get_template_components	Get all template components, including pending.
get_ts_fmt	Get the format for timestamps.
get_ts_name_fmt	Get the format for timestamps to use in names.
make_test_store_from_spec	Generate an store for testing purposes.
prepare_test_store_from_spec	Generate a valid store from a specification in terms of nested elements/iterations/EARs.
rechunk_parameter_base
rechunk_runs
reinstate_replaced_dir	Reinstate the directory containing replaced workflow details.
remove_path	Try very hard to delete a directory or file.
remove_replaced_dir	Remove the directory containing replaced workflow details.
rename_path	Revert the replaced workflow path to its original name.
save	Commit pending changes to disk, if not in batch-update mode.
set_EAR_end	Mark an element action run as finished.
set_EAR_skip	Mark an element action run as skipped.
set_EAR_start	Mark an element action run as started.
set_EAR_submission_index	Set the submission index for an element action run.
set_EARs_initialised	Mark an element action run as initialised.
set_file	Set details of a file, including whether it is associated with a parameter.
set_jobscript_metadata	Set the metadata for a job script.
set_parameter_value	Set the value of a parameter.
unzip	Convert this store into expanded form.
update_loop_num_iters	Add iterations to a loop.
update_loop_parents	Set the parents of a loop.
update_param_source	Set the source of a parameter.
using_resource	Context manager for managing StoreResource objects associated with the store.
write_empty_workflow	Write an empty persistent workflow.
zip	Convert this store into archival form.

Attributes

EAR_cache	Cache for persistent EARs.
element_cache	Cache for persistent elements.
element_iter_cache	Cache for persistent element iterations.
has_pending	Whether there are any pending changes.
is_submittable	Does this store support workflow submission?
logger	The logger to use.
num_EARs_cache	Cache for total number of persistent EARs.
num_tasks_cache	Cache for number of persistent tasks.
param_sources_cache	Cache for persistent parameter sources.
parameter_cache	Cache for persistent parameters.
task_cache	Cache for persistent tasks.
ts_fmt	The format for timestamps.
use_cache	Whether to use a cache.
workflow	The workflow this relates to.

Parameters:

• workflow (Workflow | None) –

• path (Path) –

• fs (AbstractFileSystem) –

property EAR_cache: dict[int, AnySEAR]

Cache for persistent EARs.

add_EAR(elem_iter_ID, action_idx, commands_idx, data_idx, metadata=None, save=True)

Add a new EAR to an element iteration.

Parameters:

• elem_iter_ID (int) –

• action_idx (int) –

• commands_idx (list[int]) –

• data_idx (DataIndex) –

• metadata (Metadata | None) –

• save (bool) –

Return type:

int

add_element(task_ID, es_idx, seq_idx, src_idx, save=True)

Add a new element to a task.

Parameters:

• task_ID (int) –

• es_idx (int) –

• seq_idx (dict[str, int]) –

• src_idx (dict[str, int]) –

• save (bool) –

Return type:

int

add_element_iteration(element_ID, data_idx, schema_parameters, loop_idx=None, save=True)

Add a new iteration to an element.

Parameters:

• element_ID (int) –

• data_idx (DataIndex) –

• schema_parameters (list[str]) –

• loop_idx (Mapping[str, int] | None) –

• save (bool) –

Return type:

int

add_element_set(task_id, es_js, save=True)

Add an element set to a task.

Parameters:

• task_id (int) –

• es_js (Mapping) –

• save (bool) –

add_file(store_contents, is_input, source, path, contents=None, filename=None, save=True)

Add a file that will be associated with a parameter.

Parameters:

• store_contents (bool) –

• is_input (bool) –

• source (ParamSource) –

• path (Path | str) –

• contents (str | None) –

• filename (str | None) –

• save (bool) –

add_loop(loop_template, iterable_parameters, parents, num_added_iterations, iter_IDs, save=True)

Add a new loop to the workflow.

Parameters:

• loop_template (Mapping[str, Any]) –

• parents (Sequence[str]) –

• num_added_iterations (Mapping[tuple[int, ...], int]) –

• iter_IDs (Iterable[int]) –

• save (bool) –

add_set_parameter(data, source, save=True)

Add a parameter that is set to a value.

Parameters:

• data (ParameterValue | list | tuple | set | dict | int | float | str | Any) –

• source (ParamSource) –

• save (bool) –

Return type:

int

add_submission(sub_idx, sub_js, save=True)

Add a new submission.

Parameters:

• sub_idx (int) –

• sub_js (JSONDocument) –

• save (bool) –

add_submission_part(sub_idx, dt_str, submitted_js_idx, save=True)

Add a submission part.

Parameters:

• sub_idx (int) –

• dt_str (str) –

• submitted_js_idx (list[int]) –

• save (bool) –

add_task(idx, task_template, save=True)

Add a new task to the workflow.

Parameters:

• idx (int) –

• task_template (Mapping) –

• save (bool) –

add_template_components(temp_comps, save=True)

Add template components to the workflow.

Parameters:

• temp_comps (Mapping[str, dict]) –

• save (bool) –

Return type:

None

add_unset_parameter(source, save=True)

Add a parameter that is not set to any value.

Parameters:

• source (ParamSource) –

• save (bool) –

Return type:

int

cache_ctx()

Context manager for using the persistent element/iteration/run cache.

Return type:

Iterator[None]

cached_load()

Context manager to cache the metadata.

Return type:

Iterator[None]

check_parameters_exist(ids)

For each parameter ID, return True if it exists, else False.

Parameters:

ids (Sequence[int]) –

Return type:

Iterator[bool]

copy(path=None)

Copy the workflow store.

This does not work on remote filesystems.

Parameters:

path (PathLike) –

Return type:

Path

delete()

Delete the persistent workflow.

Return type:

None

delete_no_confirm()

Permanently delete the workflow data with no confirmation.

Return type:

None

property element_cache: dict[int, AnySElement]

Cache for persistent elements.

property element_iter_cache: dict[int, AnySElementIter]

Cache for persistent element iterations.

get_EAR_skipped(EAR_ID)

Whether the element action run with the given ID was skipped.

Parameters:

EAR_ID (int) –

Return type:

bool

get_EARs(ids)

Get element action runs with the given IDs.

Parameters:

ids (Iterable[int]) –

Return type:

Sequence[AnySEAR]

get_creation_info()

Get information about the creation of the workflow.

Return type:

StoreCreationInfo

get_element_iterations(ids)

Get element iterations with the given IDs.

Parameters:

ids (Iterable[int]) –

Return type:

Sequence[AnySElementIter]

get_elements(ids)

Get elements with the given IDs.

Parameters:

ids (Iterable[int]) –

Return type:

Sequence[AnySElement]

get_loops()

Retrieve all loops, including pending.

Return type:

dict[int, LoopDescriptor]

get_loops_by_IDs(ids)

Retrieve loops by index (ID), including pending.

Parameters:

ids (Iterable[int]) –

Return type:

dict[int, LoopDescriptor]

get_name()

Get the name of the workflow.

Return type:

str

get_parameter_set_statuses(ids)

Get whether the parameters with the given IDs are set.

Parameters:

ids (Iterable[int]) –

Return type:

list[bool]

get_parameter_sources(ids)

Get the sources of the parameters with the given IDs.

Parameters:

ids (Iterable[int]) –

Return type:

list[ParamSource]

get_parameters(ids, **kwargs)

Get parameters with the given IDs.

Parameters:

ids (Iterable[int]) – The IDs of the parameters to get.

Keyword Arguments:

dataset_copy (bool) – For Zarr stores only. If True, copy arrays as NumPy arrays.

Return type:

list[AnySParameter]

get_submissions()

Retrieve all submissions, including pending.

Return type:

dict[int, JSONDocument]

get_submissions_by_ID(ids)

Get submissions with the given IDs.

Parameters:

ids (Iterable[int]) –

Return type:

dict[int, JSONDocument]

get_task(task_idx)

Get a task.

Parameters:

task_idx (int) –

Return type:

AnySTask

get_task_elements(task_id, idx_lst=None)

Get element data by an indices within a given task.

Element iterations and EARs belonging to the elements are included.

Parameters:

• task_id (int) –

• idx_lst (Iterable[int] | None) –

Return type:

Iterator[Mapping[str, Any]]

get_tasks()

Retrieve all tasks, including pending.

Return type:

list[~AnySTask]

get_tasks_by_IDs(ids)

Get tasks with the given IDs.

Parameters:

ids (Iterable[int]) –

Return type:

Sequence[AnySTask]

get_template()

Get the workflow template.

Return type:

dict[str, JSONed]

get_template_components()

Get all template components, including pending.

Return type:

dict[str, Any]

get_ts_fmt()

Get the format for timestamps.

Return type:

str

get_ts_name_fmt()

Get the format for timestamps to use in names.

Return type:

str

property has_pending: bool

Whether there are any pending changes.

property is_submittable: bool

Does this store support workflow submission?

property logger: Logger

The logger to use.

classmethod make_test_store_from_spec(app, spec, dir=None, path='test_store.json', overwrite=False, ts_fmt='%d/%m/%Y, %H:%M:%S')

Generate an store for testing purposes.

Parameters:

app (BaseApp) –

property num_EARs_cache: int | None

Cache for total number of persistent EARs.

property num_tasks_cache: int | None

Cache for number of persistent tasks.

property param_sources_cache: dict[int, ParamSource]

Cache for persistent parameter sources.

property parameter_cache: dict[int, AnySParameter]

Cache for persistent parameters.

static prepare_test_store_from_spec(task_spec)

Generate a valid store from a specification in terms of nested elements/iterations/EARs.

Parameters:

task_spec (Sequence[Mapping[str, Sequence[Mapping[str, Sequence[Mapping[str, Sequence]]]]]]) –

Return type:

tuple[list[dict], list[dict], list[dict], list[dict]]

rechunk_parameter_base(chunk_size=None, backup=True, status=True)

Parameters:

• chunk_size (int | None) –

• backup (bool) –

• status (bool) –

Return type:

Any

rechunk_runs(chunk_size=None, backup=True, status=True)

Parameters:

• chunk_size (int | None) –

• backup (bool) –

• status (bool) –

Return type:

Any

reinstate_replaced_dir()

Reinstate the directory containing replaced workflow details.

Return type:

None

remove_path(path)

Try very hard to delete a directory or file.

Dropbox (on Windows, at least) seems to try to re-sync files if the parent directory is deleted soon after creation, which is the case on a failed workflow creation (e.g. missing inputs), so in addition to catching PermissionErrors generated when Dropbox has a lock on files, we repeatedly try deleting the directory tree.

Parameters:

path (str | Path) –

Return type:

None

remove_replaced_dir()

Remove the directory containing replaced workflow details.

Return type:

None

rename_path(replaced, original)

Revert the replaced workflow path to its original name.

This happens when new workflow creation fails and there is an existing workflow with the same name; the original workflow which was renamed, must be reverted.

Parameters:

• replaced (str) –

• original (str | Path) –

Return type:

None

save()

Commit pending changes to disk, if not in batch-update mode.

Return type:

None

set_EAR_end(EAR_ID, exit_code, success, save=True)

Mark an element action run as finished.

Parameters:

• EAR_ID (int) –

• exit_code (int) –

• success (bool) –

• save (bool) –

Return type:

datetime

set_EAR_skip(EAR_ID, save=True)

Mark an element action run as skipped.

Parameters:

• EAR_ID (int) –

• save (bool) –

Return type:

None

set_EAR_start(EAR_ID, save=True)

Mark an element action run as started.

Parameters:

• EAR_ID (int) –

• save (bool) –

Return type:

datetime

set_EAR_submission_index(EAR_ID, sub_idx, save=True)

Set the submission index for an element action run.

Parameters:

• EAR_ID (int) –

• sub_idx (int) –

• save (bool) –

Return type:

None

set_EARs_initialised(iter_ID, save=True)

Mark an element action run as initialised.

Parameters:

• iter_ID (int) –

• save (bool) –

Return type:

None

set_file(store_contents, is_input, param_id, path, contents=None, filename=None, clean_up=False, save=True)

Set details of a file, including whether it is associated with a parameter.

Parameters:

• store_contents (bool) –

• is_input (bool) –

• param_id (int | None) –

• path (Path | str) –

• contents (str | None) –

• filename (str | None) –

• clean_up (bool) –

• save (bool) –

set_jobscript_metadata(sub_idx, js_idx, version_info=None, submit_time=None, submit_hostname=None, submit_machine=None, submit_cmdline=None, os_name=None, shell_name=None, scheduler_name=None, scheduler_job_ID=None, process_ID=None, save=True)

Set the metadata for a job script.

Parameters:

• sub_idx (int) –

• js_idx (int) –

• version_info (VersionInfo | None) –

• submit_time (str | None) –

• submit_hostname (str | None) –

• submit_machine (str | None) –

• submit_cmdline (list[str] | None) –

• os_name (str | None) –

• shell_name (str | None) –

• scheduler_name (str | None) –

• scheduler_job_ID (str | None) –

• process_ID (int | None) –

• save (bool) –

set_parameter_value(param_id, value, is_file=False, save=True)

Set the value of a parameter.

Parameters:

• param_id (int) –

• value (Any) –

• is_file (bool) –

• save (bool) –

property task_cache: dict[int, AnySTask]

Cache for persistent tasks.

property ts_fmt: str

The format for timestamps.

unzip(path='.', log=None)

Convert this store into expanded form.

Parameters:

• path (str) –

• log (str | None) –

Return type:

str

update_loop_num_iters(index, num_added_iters, save=True)

Add iterations to a loop.

Parameters:

• index (int) –

• num_added_iters (Mapping[tuple[int, ...], int]) –

• save (bool) –

Return type:

None

update_loop_parents(index, num_added_iters, parents, save=True)

Set the parents of a loop.

Parameters:

• index (int) –

• num_added_iters (Mapping[tuple[int, ...], int]) –

• parents (Sequence[str]) –

• save (bool) –

Return type:

None

update_param_source(param_sources, save=True)

Set the source of a parameter.

Parameters:

• param_sources (Mapping[int, ParamSource]) –

• save (bool) –

Return type:

None

property use_cache: bool

Whether to use a cache.

using_resource(res_label, action)

Context manager for managing StoreResource objects associated with the store.

Parameters:

• res_label (str) –

• action (str) –

Return type:

Iterator[Any]

property workflow: Workflow

The workflow this relates to.

classmethod write_empty_workflow(app, *, template_js, template_components_js, wk_path, fs, name, replaced_wk, creation_info, ts_fmt, ts_name_fmt)

Write an empty persistent workflow.

Parameters:

• app (BaseApp) –

• template_js (TemplateMeta) –

• template_components_js (dict[str, Any]) –

• wk_path (str) –

• fs (AbstractFileSystem) –

• name (str) –

• replaced_wk (str | None) –

• creation_info (StoreCreationInfo) –

• ts_fmt (str) –

• ts_name_fmt (str) –

Return type:

None

zip(path='.', log=None, overwrite=False, include_execute=False, include_rechunk_backups=False)

Convert this store into archival form.

Parameters:

• path (str) –

• log (str | None) –

Return type:

str